Sequence
atgc intronic sequence ATGC exonic sequence...gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgttatagcttttttgagcttcatttgtaagaaaatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG
Basic information
species | Glycine max |
transcript | GLYMA12G07910.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G07910.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
--gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgttatagcttttttgagcttcatttg---taagaaaatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG
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gtgagtaaacttaaaatt-ttctattcattgattaaaatataatatatctatctga--tttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
upper sequence: GLYMA12G07910.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 4
gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgttatagcttttttgagcttcatttgtaagaaaatgctc-gcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG
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---gtacctaaaacagtcaggaaccatgattttttattgacagaataatagtgtcttaccttgatgatttactaaacaatataagagtcactattttgcagGGTAGAGCCAGGGAAGCTGGTGAGATCAACAAAAGTTTGCTCACACTTGGACGTGTCATAAATGCTTTGGTTGAACACTCTGGTCACATTCCATATAG
upper sequence: GLYMA12G07910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 5
gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgttatagctttt--ttgagcttcatttgtaagaa---aatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG
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-----acaacaaaagcatatgcataatatgaagttgtgtgttaggcaatgaaaagttcatttatcttcacataaaagtttgactgcaaaaattcaatgctttcagGGCAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACTCTTGGGCGTGTTATTAATGCGCTGGTTGAGCACTCTGGTCATGTTCCATATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagactaaaatgttatagcttttttgagcttcatttgtaagaaaatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG
gactaaa putative branch site (score: 2)
atttgtaagaaaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgttatagcttttttgagcttcatttgtaagaaaatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG
- - - - - - -ctcactc
- - - - - - - - - - - - - - - - - - -ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcttca